| Title | Prefix | Description | Official page | |
|---|---|---|---|---|
| Agronomy Ontology | AGRO | Ontology of concepts relevant to agronomy experiments. | https://github.com/AgriculturalSemantics/agro | |
| An ontology of core ecological entities | ECOCORE | An ontology for ecological entities. | https://github.com/EcologicalSemantics/ecocore | |
| Anatomical Entity Ontology | AEO | Ontology of anatomical structures that expand CARO, the Common Anatomy Reference Ontology. | https://github.com/obophenotype/human-developmental-anatomy-ontology/ | |
| Antibiotic Resistance Ontology | ARO | Ontology for antibiotic resistance genes and mutations. | https://github.com/arpcard/aro | |
| Apollo Structured Vocabulary [1] | APOLLO-SV | Ontology for enabling interoperability of epidemic models and public health application software. | https://github.com/ApolloDev/apollo-sv | |
| Ascomycete phenotype ontology | APO | A structured controlled vocabulary for the phenotypes of Ascomycete fungi. | http://www.yeastgenome.org/ | |
| Basic Formal Ontology[2] | BFO | The upper-level ontology upon which OBO Foundry ontologies are built. | http://ifomis.org/bfo/ | |
| Beta Cell Genomics Ontology | BCGO | An application ontology built for beta cell genomic studies. | https://github.com/obi-bcgo/bcgo | |
| Biological Collections Ontology [3] | BCO | An ontology for biodiversity data. | https://github.com/tucotuco/bco | |
| Biological Imaging Methods Ontology | FBBI | Ontology for methods involved in biomedical imaging, including preparation and acquisition. | http://cellimagelibrary.org/ | |
| Biological Spatial Ontology | BSPO | An ontology for representing spatial concepts used in biology. | https://github.com/obophenotype/biological-spatial-ontology | |
| BRENDA tissue / enzyme source | BTO | An ontology for the source of enzymes. | http://www.brenda-enzymes.org | |
| C. elegans development ontology (see WormBase) | WBLS | An ontology for the development of Caenorhabditis elegans. | https://web.archive.org/web/20170420234209/http://www.wormbase.org/ | |
| C. elegans Gross Anatomy Ontology (see WormBase) | WBBT | An ontology for the anatomy of Caenorhabditis elegans. | https://web.archive.org/web/20170420234209/http://www.wormbase.org/ | |
| C. elegans phenotype (see WormBase) | WBPHENOTYPE | An ontology for the phenotypes of Caenorhabditis elegans. | https://github.com/obophenotype/c-elegans-phenotype-ontology | |
| Cardiovascular Disease Ontology | CVDO | An ontology for concepts related to cardiovascular diseases. | http://code.google.com/p/cvdo https://github.com/OpenLHS/CVDO | |
| Cell Line Ontology [4] | CLO | Ontology to describe cell lines. | http://purl.bioontology.org/ontology/CLO http://www.clo-ontology.org | |
| Cell Ontology [5] | CL | Ontology for metazoan cell types. | http://obofoundry.org/ontology/cl.html https://github.com/obophenotype/cell-ontology | |
| Chemical Entities of Biological Interest | CHEBI | Ontology of small molecular entities of biological interest. | http://www.ebi.ac.uk/chebi | |
| Chemical Information Ontology [6] | CHEMINF | Ontology for descriptors used in chemoinformatics databases. | https://github.com/egonw/semanticchemistry https://github.com/semanticchemistry/semanticchemistry | |
| Chemical Methods Ontology | CHMO | An ontology for the methods used in chemical experiments. | https://github.com/rsc-ontologies/rsc-cmo | |
| Clinical LABoratory Ontology | LABO | An ontology of prescriptions and reports in clinical laboratories. | https://github.com/OpenLHS/LABO | |
| Clinical measurement ontology [7] | CMO | Ontology to classify clinical measurements of experimental animals. | http://rgd.mcw.edu/rgdweb/ontology/search.html | |
| Common Anatomy Reference Ontology [8] | CARO | An ontology to improve interoperability between anatomy ontologies for different organisms. | https://github.com/obophenotype/caro/ | |
| Comparative Data Analysis Ontology [9] | CDAO | Ontology of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees. | https://bioportal.bioontology.org/ontologies/CDAO https://github.com/evoinfo/cdao | |
| Confidence Information Ontology [10] | CIO | An ontology to describe confidence information in sequence annotations. | https://github.com/BgeeDB/confidence-information-ontology | |
| Contributor Role Ontology | CRO | An ontology for the diverse roles behind a scientific research article. | https://data2health.github.io/contributor-role-ontology/ https://github.com/data2health/contributor-role-ontology | |
| Ctenophore Ontology | CTENO | An anatomical and developmental ontology for ctenophores (Comb Jellies). | https://github.com/obophenotype/ctenophore-ontology | |
| Dictyostelium discoideum anatomy[11] | DDANAT | A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum. | http://dictybase.org/ | |
| Dictyostelium discoideum phenotype ontology | DDPHENO | An ontology for phenotypes of the slime-mould Dictyostelium discoideum. | http://dictybase.org/ | |
| Drosophila development | FBDV | An ontology of the development of Drosophila melanogaster. | http://purl.obolibrary.org/obo/fbdv | |
| Drosophila gross anatomy[12] | FBBT | An ontology for the anatomy of Drosophila melanogaster. | http://purl.obolibrary.org/obo/fbbt | |
| Drosophila Phenotype Ontology | FBCV | An ontology of common Drosophila phenotypes. | http://purl.obolibrary.org/obo/fbcv | |
| Drug-drug Interaction and Drug-drug Interaction Evidence Ontology [13] | DIDEO | Ontology for drug–drug interaction evidence. | https://github.com/DIDEO/DIDEO | |
| Evidence & Conclusion Ontology[14] | ECO | An ontology for types evidence used to support scientific claims. | https://github.com/evidenceontology/evidenceontology/ | |
| eagle-i resource ontology | ERO | An ontology of research equipment, protocols and consumables. | https://open.med.harvard.edu/wiki/display/eaglei/Ontologyhttps://www.eagle-i.net/ | |
| Emotion Ontology [15] | MFOEM | An ontology of emotions, moods, and other kinds of feelings. | https://github.com/jannahastings/emotion-ontology | |
| Environment Ontology [16] | ENVO | Ontology of environmental features and habitats. | http://environmentontology.org/ | |
| Experimental condition ontology [17] | XCO | An ontology for the different conditions in which experimental measurements are taken. | https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 | |
| Exposure Ontology [18] | EXO | Ontology to describe exposure to environmental factors (such as cigarette smoke) that might influence clinical outcomes. | http://ctdbase.org/help/exposureHelp.jsp | |
| Fission Yeast Phenotype Ontology[19] | FYPO | An ontology of phenotypes of fission yeast. | http://www.pombase.org/documentation/gene-page-phenotypes https://github.com/pombase/fypo | |
| Flora Phenotype Ontology [20] | FLOPO | An ontology for traits and phenotypes of flowering plants. | https://github.com/flora-phenotype-ontology/flopoontology | |
| FlyBase Controlled Vocabulary | FBCV | An ontology to support the FlyBase project. | http://purl.obolibrary.org/obo/fbcv | |
| Food Ontology [21] | FOODON | An ontology to represent entities that play a food role or related to foods. | https://foodon.org/ | |
| Foundational Model of Anatomy Ontology (subset) | FMAO | Subset of the Foundational Model of Anatomy Ontology. | http://si.washington.edu/projects/fma | |
| Fungal Anatomy Ontology | FAO | An ontology for the anatomy of fungi. | https://github.com/obophenotype/fungal-anatomy-ontology/ | |
| Gazetteer | GAZ | An ontology that acts as a gazetteer (geographical dictionary). | http://environmentontology.github.io/gaz/ | |
| Gene Ontology | GO | An ontology for describing the function of genes and gene products. | http://geneontology.org http://geneontology.org/ | |
| Genomic Epidemiology Ontology [22] | GENEPIO | An ontology for foodborne pathogens and associated outbreaks. | http://genepio.github.io/genepio | |
| Genotype Ontology | GENO | An ontology for genotypes and their related phenotypes and diseases. | https://github.com/monarch-initiative/GENO-ontology/ | |
| Geographical Entity Ontology | GEO | An ontology of geographical entities. | https://github.com/ufbmi/geographical-entity-ontology/wiki | |
| Glycan Naming Ontology [23] | GNOME | An ontology for glycans based on GlyTouCan. | https://github.com/glygen-glycan-data/GNOme | |
| Homology Ontology [24] | HOM | An ontology for concepts related to homology. | https://github.com/BgeeDB/homology-ontology | |
| Human Ancestry Ontology [25] | HANCESTRO | An ontology of ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. | https://github.com/EBISPOT/ancestro | |
| Human Developmental Stages | HSAPDV | An ontology of stages of the human life. | https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv | |
| Human Disease Ontology | DO | An ontology for describing human diseases. | http://www.disease-ontology.org | |
| Human Phenotype Ontology | HPO | An ontology for human phenotypes in hereditary and non-hereditary diseases. | https://hpo.jax.org/app/ http://www.human-phenotype-ontology.org/ | |
| HUPO-PSI cross-linking and derivatization reagents controlled vocabulary | PSI-MS | An ontology for reagents used to cross-link molecules in mass spectrometry experiments. | http://www.psidev.info/groups/controlled-vocabularies | |
| Hymenoptera Anatomy Ontology [26] | HAO | An ontology of the anatomy of the Hymenoptera (bees, wasps, and ants). | http://hymao.org | |
| Hypertension Ontology | HTN | An ontology for clinical data about hypertension. | https://github.com/aellenhicks/htn_owl | |
| Infectious Disease Ontology [27] | IDO | A set of ontologies related to infectious diseases. | http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology | |
| Information Artifact Ontology | IAO | An ontology of information entities. | https://github.com/information-artifact-ontology/IAO/ | |
| Informed Consent Ontology | ICO | An ontology for concepts related to informed consent, such as forms and policies. | https://github.com/ICO-ontology/ICO | |
| Integrative and Conjugative Element Ontology | ICEO | An ontology of bacterial integrative and conjugative elements (ICEs). | https://github.com/ontoice/ICEO | |
| Interaction Network Ontology [28] | INO | An ontology for gene-gene interactions. | https://github.com/INO-ontology/ino | |
| Malaria Ontology [29] | IDOMAL | An ontology for concepts related to malaria. | https://www.vectorbase.org/ontology-browser | |
| Mammalian Feeding Muscle Ontology | MFMO | An ontology for the mammalian muscles that play a role in feeding behavior. | https://github.com/rdruzinsky/feedontology | |
| Mammalian Phenotype Ontology | MP | Standard terms for annotating mammalian phenotypic data. | http://www.informatics.jax.org/searches/MP_form.shtml | |
| Mass spectrometry ontology | MI | An ontology for concepts to describe mass spectrometry in the context of proteomics. | http://www.psidev.info/groups/controlled-vocabularies | |
| Measurement method ontology | MMO | An ontology for methods of clinical and laboratory measurements. | https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 | |
| Medaka Developmental Stages | OlatDv | An ontology of life stages for the medaka fish. | https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv | |
| Mental Disease Ontology [30] | MFOMD | An ontology for mental diseases. | https://github.com/jannahastings/mental-functioning-ontology | |
| Mental Functioning Ontology | MFO | An ontology for concepts related to mental functioning. | http://code.google.com/p/mental-functioning-ontology https://github.com/jannahastings/mental-functioning-ontology | |
| MHC Restriction Ontology [31] | MRO | An ontology for Major Histocompatibility Complex (MHC) restriction in experiments. | https://github.com/IEDB/MRO | |
| MIAPA Ontology [32] | MIAPA | An ontology for phylogenetic data. | http://www.evoio.org/wiki/MIAPA | |
| Microbial Conditions Ontology [33] | MCO | An ontology for microbial growth conditions. | https://github.com/microbial-conditions-ontology/microbial-conditions-ontology | |
| Minimum PDDI Information Ontology | MPIO | An ontology of the minimum information to describe drug–drug interactions. | https://github.com/MPIO-Developers/MPIO | |
| Molecular Interactions Controlled Vocabulary | MI | An ontology for concepts related to the study of protein-protein interactions. | https://github.com/HUPO-PSI/psi-mi-CV | |
| Mondo Disease Ontology | MONDO | An ontology for the integration of information on disease. | https://monarch-initiative.github.io/mondo | |
| Mosquito gross anatomy ontology (VectorBase) | TGMA | An ontology for the anatomy of mosquitoes. | http://anobase.vectorbase.org | |
| Mouse adult gross anatomy ontology | EMAPA | An ontology for the adult anatomy of the mouse (Mus). | https://github.com/obophenotype/mouse-anatomy-ontology | |
| Mouse Developmental Stages | MmusDv | An ontology of stages of the mouse (Mus) life. | https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv | |
| Mouse gross anatomy and development, timed | EMAP | Ontology of anatomical structures of the mouse (Mus musculus). | http://emouseatlas.org | |
| Mouse Pathology Ontology [34] | MPATH | An ontology of mouse pathology phenotypes. | http://www.pathbase.net | |
| Name Reaction Ontology | RXNO | An ontology for organic reactions in organic synthesis. | https://github.com/rsc-ontologies/rxno | |
| NCBI organismal classification [35] | NCBITaxon | An ontology representation of the NCBI organismal taxonomy. | https://github.com/obophenotype/ncbitaxon | |
| Neuro Behavior Ontology | NBO | An ontology of behavioral phenotypes of animals. | https://github.com/obo-behavior/behavior-ontology/ | |
| NOMEN - A nomenclatural ontology for biological names [36] | NOMEN | An ontology of the rules of nomenclature for biological names. | https://github.com/SpeciesFileGroup/nomen | |
| Non-Coding RNA Ontology [37] | NCRO | An ontology for non-coding RNA function. | https://github.com/OmniSearch/ncro | |
| Ontologized MIABIS | OMIABIS | An ontological version of MIABIS (Minimum Information About BIobank data Sharing). | https://github.com/OMIABIS/omiabis-dev | |
| Ontology for Biobanking [38] | OBIB | An ontology for concepts related to biobanks. | https://github.com/biobanking/biobanking/wiki | |
| Ontology for Biomedical Investigations | OBI | An ontology which describes biological processes, cellular components and molecular functions in living organisms. | http://obi-ontology.org | |
| Ontology for General Medical Science | OGMS | An ontology for general aspects of medicine, with a focus on cancer. | https://github.com/OGMS/ogms | |
| Ontology for Parasite LifeCycle [39] | OPL | A reference ontology for parasite life cycle stages. | https://github.com/OPL-ontology/OPL | |
| Ontology of Adverse Events [40] | OAE | An ontology for adverse events of drug regimens. | https://github.com/OAE-ontology/OAE/ | |
| Ontology of Arthropod Circulatory Systems [41] | OARCS | An ontology for the circulatory systems of arthropods. | https://github.com/aszool/oarcs | |
| Ontology of Biological and Clinical Statistics [42] | OBCS | An ontology to describe statistical tools and methods used in biomedical investigation. | https://github.com/obcs/obcs | |
| Ontology of Biological Attributes | OBA | An ontology for biological traits. | https://github.com/obophenotype/bio-attribute-ontology | |
| Ontology of Medically Related Social Entities [43] | OMRSE | An ontology for entities (roles and organizations) related to healthcare. | https://ontology.atlassian.net/wiki/display/OMRSE/OMRSE+Home https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview | |
| Ontology of Microbial Phenotypes [44] | OMP | An ontology of phenotypes of microorganisms. | http://microbialphenotypes.org | |
| Ontology of Organizational Structures of Trauma centers and Trauma systems | OOSTT | An ontology for the organizational structures of trauma centers and trauma systems. | https://github.com/OOSTT/OOSTT | |
| Ontology of Precision Medicine and Investigation | OPMI | An ontology for concepts related to precision medicine. | https://github.com/OPMI/opmi | |
| Ontology of Prokaryotic Phenotypic and Metabolic Characters [45] | MICRO | An ontology of prokaryotic phenotypic and metabolic characters. | https://github.com/carrineblank/MicrO | |
| Ontology of RNA Sequencing | ORNASEQ | An ontology to annotate RNA Sequencing experiments. | http://kim.bio.upenn.edu/software/ornaseq.shtml | |
| Ontology of Vaccine Adverse Events [46] | OVAE | An ontology for adverse events of vaccines. | http://www.ontobee.org/browser/index.php?o=OVAE http://www.violinet.org/ovae/ | |
| Pathogen Host Interaction Phenotype Ontology | PHIPO | An ontology of phenotypes that occur in pathogen-host interactions. | https://github.com/PHI-base/phipo | |
| Pathogen Transmission Ontology | TRANS | An ontology for disease transmissio | https://github.com/DiseaseOntology/PathogenTransmissionOntology | |
| Pathway ontology | PW | An ontology for annotating gene products to pathways. | http://rgd.mcw.edu/rgdweb/ontology/search.html | |
| Performance Summary Display Ontology | PSDO | An ontology for concepts related to performance information for teams and organizations. | https://github.com/Display-Lab/psdo | |
| Phenotype And Trait Ontology | FOBI | FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data. | https://github.com/pcastellanoescuder/FoodBiomarkerOntology | |
| Planaria Ontology | PLANA | An ontology for the anatomy and developmental stages of the planaria (Schmidtea mediterranea). | https://github.com/obophenotype/planaria-ontology | |
| Planarian Phenotype Ontology | PLANP | An ontology for phenotypes of the planaria (Schmidtea mediterranea). | https://github.com/obophenotype/planarian-phenotype-ontology | |
| Plant Experimental Conditions Ontology | PECO | An ontology for concepts related to plant biology experiments. | http://planteome.org/ | |
| Plant ontology | PO | An ontology and database resource that links plant traits to genomics data. | http://browser.planteome.org/amigo | |
| Plant Phenology Ontology | PPO | An ontology for describing the cyclic phenomena of plants. | https://github.com/PlantPhenoOntology/PPO | |
| Plant Trait Ontology | TO | An ontology for phenotypic traits in plants. | http://browser.planteome.org/amigo | |
| Platynereis Developmental Stages | PDUMDV | An ontology for life stages of the annelid Platynereis dumerilii. | https://github.com/obophenotype/developmental-stage-ontologies/wiki | |
| Population and Community Ontology | PCO | An ontology for describing groups of interacting organisms. | https://github.com/PopulationAndCommunityOntology/pco | |
| Porifera Ontology [47] | PORO | An ontology for the anatomy of sponges (Porifera) | https://github.com/obophenotype/porifera-ontology | |
| Protein modification [48] | MOD | An ontology for protein chemical modifications. | https://web.archive.org/web/20130815050612/http://www.psidev.info/MOD | |
| Protein Ontology [49] | PRO | An ontological representation of protein-related entities. | http://proconsortium.org | |
| Rat Strain Ontology [50] | RS | An ontology for laboratorial rat strains. | http://rgd.mcw.edu/rgdweb/search/strains.html | |
| Relation Ontology [51] | RO | An ontology for relations between terms in the ontologies. | https://github.com/oborel/obo-relations/ | |
| Scientific Evidence and Provenance Information Ontology | SEPIO | An ontology for the provenance of scientific claims and supporting evidence. | https://github.com/monarch-initiative/SEPIO-ontology | |
| Sequence types and features ontology | SO | An ontology for annotation of sequences. | https://github.com/The-Sequence-Ontology/SO-Ontologies | |
| Software Ontology[52] | SWO | An ontology to describe software applications with a focus on bioinformatics tools. | https://github.com/allysonlister/swo | |
| Spider Ontology[53] | SPD | An ontology for anatomy and behavior of spiders as well as spider-derived products. | http://www.ontobee.org/ontology/SPD | |
| Symptom Ontology | SYMP | An ontology of disease symptoms. | http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page | |
| Taxonomic rank vocabulary | TAXRANK | An ontology of taxonomic ranks in systematics. | https://github.com/phenoscape/taxrank | |
| Teleost taxonomy ontology [54] | TTO | An ontology for the taxonomy of teleost fish. | https://github.com/phenoscape/teleost-taxonomy-ontology | |
| The Data Use Ontology [55] | DUO | Ontology for conditions of data use. | https://github.com/EBISPOT/DUO | |
| The Drug Ontology [56] | DRON | An ontology for drug products. | https://bitbucket.org/uamsdbmi/dron.git | |
| The Ontology of Genes and Genomes | OGG | An ontology of genes and genomes of biological organisms. | https://bitbucket.org/hegroup/ogg | |
| The Oral Health and Disease Ontology [57] | OHD | An ontology for the content of teeth-related health records. | https://purl.obolibrary.org/obo/ohd/home | |
| The Prescription of Drugs Ontology [58] | PDRO | An ontology for concepts related to prescription of drugs. | https://github.com/OpenLHS/PDRO | |
| The Statistical Methods Ontology | STATO | An ontology for statistical methods, such as tests and experimental designs. | http://stato-ontology.org/ | |
| Tick Anatomy Ontology [59] | TADS | An ontology for the anatomy of the tick families Ixodidae and Argasidae. | https://www.vectorbase.org/ontology-browser | |
| Uberon multi-species anatomy ontology | UBERON | An integrative, cross species ontology for anatomical terms. | http://uberon.org | |
| Unified phenotype ontology (uPheno) | UPHENO | An ontology for unified phenotypical descriptictions. | https://github.com/obophenotype/upheno | |
| Units of measurement ontology | UO | An ontology of metrical units, couplet to the PATO ontology. | https://github.com/bio-ontology-research-group/unit-ontology | |
| Vaccination Informed Consent Ontology [60] | VICO | An ontology of clinical informed consents focused on vaccination procedures. | https://github.com/ICO-ontology/ICO | |
| Vaccine Ontology [61] | VO | An ontology for concepts related to vaccines and vaccination. | http://www.violinet.org/vaccineontology | |
| Vertebrate Taxonomy Ontology | VTO | An ontology for the taxonomy of vertebrates. | https://github.com/phenoscape/vertebrate-taxonomy-ontology | |
| Vertebrate Trait Ontology | VT | An ontology for traits covering vertebrates | https://github.com/AnimalGenome/vertebrate-trait-ontology | |
| VEuPathDB ontology | EUPATH | An ontology for the support of the Eukaryotic Pathogen, Host & Vector Genomics Resource. | https://github.com/VEuPathDB-ontology/VEuPathDB-ontology | |
| Xenopus Anatomy Ontology [62] | XAO | Ontology of the anatomy of the African clawed frog (Xenopus laevis). | http://www.xenbase.org/anatomy/xao.do?method=display | |
| Xenopus Phenotype Ontology | XPO | An ontology for anatomical, cellular, and gene function phenotypes in African clawed frogs (Xenopus laevis). | https://github.com/obophenotype/xenopus-phenotype-ontology | |
| Zebrafish anatomy and development ontology | ZFA | Ontology for the anatomy and development of the zebrafish (Danio rerio). | https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources | |
| Zebrafish developmental stages ontology | ZFS | An ontology for developmental stages of the zebrafish (Danio rerio). | https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources | |
| Zebrafish Experimental Conditions Ontology | ZECO | An ontology for experimental conditions used in zebrafish research and described in ZFIN. | https://github.com/ybradford/zebrafish-experimental-conditions-ontology | |
| Zebrafish Phenotype Ontology | ZP | An ontology for the phenotypes of the zebrafish (Danio rerio). | https://github.com/obophenotype/zebrafish-phenotype-ontology |